This study concerns the synthesis, structure and reactivity of nitrosyl complexes of ruthenium and osmium. Attempts have been made to prepare coordinatively saturated and unsaturated complexes and a study of their oxidative addition reactions bears considerable resemblance to the more familiar carbonyl complexes M(CO)3(PPh3)2. A number of interesting atom transfer reactions, generally involving oxygen, have been observed. The d8 complex RuCl(CO)(NO)(PPh3)2 results from the interaction of RuHCl(CO)(PPh3)3 with N-methyl-N-nitrosotoluene-p-sulphonamide. The labile halide ligand is readily displaced by a large range of anions and it is believed that both linear and bent nitrosyl linkages may exist for different members of this series. The structures of these complexes are discussed in the light of recent X-ray crystal structure data. Halogens and hydrogen halides add to give the familiar RuX3(NO)(PPh3)2; RuCl3(NO)(PPh2Me)2 is prepared in a direct reaction and also by phosphine exchange and 1H n.m.r. data confirm that the phosphine ligands are trans. The complexes RuX(CO)(NO)(PPh3)2 react readily with O2 to form the dioxygen complexes Ru(O2)X(NO)(PPh3)2. Halogens and hydrogen halides produce RuX3(NO)(PPh3)2. The dioxygen complexes react with SO2 and N2O4 to give sulphato and dinitrato complexes respectively. The reaction with CO results in the intramolecular oxidation of the nitrosyl group to coordinated nitrate accompanied by the incorporation of two moles of CO, i.e. RuX(NO3)(CO)2(PPh3)2 is formed. The dioxygen complexes catalytically oxidise triphenylphosphine or triphenylarsine to the respective oxides and RuX(NO)(PPh3)2 can be isolated from this cycle. Reactions of these four-coordinated complexes with O2, CO, Cl2 and NOBF4 are recorded. The dinitrosyl complex Ru(NO)2(PPh3)2 is reported from a number of syntheses, the most successful being via a ligand reaction when RuCl2(CO)2(PPh3)2 is heated with NaNO2 and Ph3P in dimethyl formamide. The P-tolyldiphenylphosphine analogue is also reported and the mono-substituted product Ru(NO)2(PPh3)[P(OPh)3] is produced in an exchange reaction between Ru(NO)2(PPh3)2 and excess triphenylphosphite. This phosphite complex reacts with Ph3P and O2 to produce Ru(O2)(NO2)(NO)PPh3)2 by an atom transfer process. Ru(NO)2(PPh3)2 reacts with the acids HY (Y = BF4, PF6, ClO4) and O2 to give the dinitrosyl cations [Ru(OH)(NO)2(PPh3)2]+Y- in which the two nitrosyl groups are structurally and electronically inequivalent. [RuCl(NO)2(PPh3)2]BF4 is reported and reactions of these dinitrosyl cations with halide ions to give RuX2(NO3)(NO)(PPh3)2, with intramolecular oxidation of the NO group, are also described. OsCl2(OH)(NO)(PPh3)2 reacts irreversibly with alcohols to form OsCl2(OR)(NO)(PPh3)2 (R = CH3, C2H5, n-C3H7, (CH3O)CH2CH2) which readily undergo hydride abstraction to form OsHCl2(NO)(PPh3)2. Sodium borohydride converts this complex to the trihydrido species OsH3(NO)(PPh3)2 and if the reaction is performed in the presence of Ph3P, OsH(NO)(PPh3)3 results. The coordinated perchlorate complex OsHCl(OClO3)(NO)(PPh3)2 results form the reaction of OsHCl2(NO)(PPh3)2 with silver perchlorate; this is readily reversed by chloride ions or the solvents CH2Cl2 and CHCl3. This perchlorato complex also arises from the reaction of OsH(CO)(NO)(PPh3)2 with HClO4 and a related tetrafluoroborato complex, OsH(OC2H5)(FBF3)(NO)(PPh3)2 by substituting HBF4. This complex reacts with Ph3P to give [OsH(OH)(NO)(PPh3)3]BF4, CO to give [Os(CO)2(NO)(PPh3)2]BF4 and LiX (X = Br, I) to give OsHX2(NO)(PPh3)2. OsHCl(OClO3)(NO)(PPh3)2 reacts with NaOH in methanol, in the presence of O2 to produce Os(O2)Cl(NO)(PPh3)2. This dioxygen complex is far less stable than the ruthenium analogue but it undergoes similar reactions. Ph3P is oxidised, SO2 and CO give sulphato and a nitratodicarbonyl complex respectively. Infra-red, 1H n.m.r., conductivity, molecular weight data and elemental analysis have been used in formulation and structural assignment.

This study concerns the synthesis, structure and reactivity of nitrosyl complexes of ruthenium and osmium. Attempts have been made to prepare coordinatively saturated and unsaturated complexes and a study of their oxidative addition reactions bears considerable resemblance to the more familiar carbonyl complexes M(CO)3(PPh3)2. A number of interesting atom transfer reactions, generally involving oxygen, have been observed. The d8 complex RuCl(CO)(NO)(PPh3)2 results from the interaction of RuHCl(CO)(PPh3)3 with N-methyl-N-nitrosotoluene-p-sulphonamide. The labile halide ligand is readily displaced by a large range of anions and it is believed that both linear and bent nitrosyl linkages may exist for different members of this series. The structures of these complexes are discussed in the light of recent X-ray crystal structure data. Halogens and hydrogen halides add to give the familiar RuX3(NO)(PPh3)2; RuCl3(NO)(PPh2Me)2 is prepared in a direct reaction and also by phosphine exchange and 1H n.m.r. data confirm that the phosphine ligands are trans. The complexes RuX(CO)(NO)(PPh3)2 react readily with O2 to form the dioxygen complexes Ru(O2)X(NO)(PPh3)2. Halogens and hydrogen halides produce RuX3(NO)(PPh3)2. The dioxygen complexes react with SO2 and N2O4 to give sulphato and dinitrato complexes respectively. The reaction with CO results in the intramolecular oxidation of the nitrosyl group to coordinated nitrate accompanied by the incorporation of two moles of CO, i.e. RuX(NO3)(CO)2(PPh3)2 is formed. The dioxygen complexes catalytically oxidise triphenylphosphine or triphenylarsine to the respective oxides and RuX(NO)(PPh3)2 can be isolated from this cycle. Reactions of these four-coordinated complexes with O2, CO, Cl2 and NOBF4 are recorded. The dinitrosyl complex Ru(NO)2(PPh3)2 is reported from a number of syntheses, the most successful being via a ligand reaction when RuCl2(CO)2(PPh3)2 is heated with NaNO2 and Ph3P in dimethyl formamide. The P-tolyldiphenylphosphine analogue is also reported and the mono-substituted product Ru(NO)2(PPh3)[P(OPh)3] is produced in an exchange reaction between Ru(NO)2(PPh3)2 and excess triphenylphosphite. This phosphite complex reacts with Ph3P and O2 to produce Ru(O2)(NO2)(NO)PPh3)2 by an atom transfer process. Ru(NO)2(PPh3)2 reacts with the acids HY (Y = BF4, PF6, ClO4) and O2 to give the dinitrosyl cations [Ru(OH)(NO)2(PPh3)2]+Y- in which the two nitrosyl groups are structurally and electronically inequivalent. [RuCl(NO)2(PPh3)2]BF4 is reported and reactions of these dinitrosyl cations with halide ions to give RuX2(NO3)(NO)(PPh3)2, with intramolecular oxidation of the NO group, are also described. OsCl2(OH)(NO)(PPh3)2 reacts irreversibly with alcohols to form OsCl2(OR)(NO)(PPh3)2 (R = CH3, C2H5, n-C3H7, (CH3O)CH2CH2) which readily undergo hydride abstraction to form OsHCl2(NO)(PPh3)2. Sodium borohydride converts this complex to the trihydrido species OsH3(NO)(PPh3)2 and if the reaction is performed in the presence of Ph3P, OsH(NO)(PPh3)3 results. The coordinated perchlorate complex OsHCl(OClO3)(NO)(PPh3)2 results form the reaction of OsHCl2(NO)(PPh3)2 with silver perchlorate; this is readily reversed by chloride ions or the solvents CH2Cl2 and CHCl3. This perchlorato complex also arises from the reaction of OsH(CO)(NO)(PPh3)2 with HClO4 and a related tetrafluoroborato complex, OsH(OC2H5)(FBF3)(NO)(PPh3)2 by substituting HBF4. This complex reacts with Ph3P to give [OsH(OH)(NO)(PPh3)3]BF4, CO to give [Os(CO)2(NO)(PPh3)2]BF4 and LiX (X = Br, I) to give OsHX2(NO)(PPh3)2. OsHCl(OClO3)(NO)(PPh3)2 reacts with NaOH in methanol, in the presence of O2 to produce Os(O2)Cl(NO)(PPh3)2. This dioxygen complex is far less stable than the ruthenium analogue but it undergoes similar reactions. Ph3P is oxidised, SO2 and CO give sulphato and a nitratodicarbonyl complex respectively. Infra-red, 1H n.m.r., conductivity, molecular weight data and elemental analysis have been used in formulation and structural assignment.

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This study concerns halogen bonding between small molecules. Except where otherwise stated herein this investigation was performed exclusively using the M06-2X density functional, in conjunction with the 6-31+G* basis set except for iodine and astatine which were treated using the aug-cc-pVDZ-PP basis set with relativistic pseudopotentials. All calculations were performed in the gas phase. The counterpoise procedure was employed for all full geometry optimisations. Statistical analysis of the Cambridge Structural Database, wherein the frequency of structures as a function of halogen bond angle and distance constituted the sole part of this study not to be based on density functional theory. Except in chapter 5, all halogens from fluorine to astatine are investigated. In chapter 3, halogen bonding between halobenzene and a single water molecule is discussed. Competition between R – X•••OH2 halogen bonding and R – X•••H-O-H hydrogen bonding interactions is described. This system is analogous to the more elaborate microsolvated 1- methyl-5-halouracil system described in chapter 4. In this latter system one 1-methyl-5- halouracil molecule interacts with either one or two water molecules. A central feature of the investigation into this system is competition between R – X•••OH2 and R=O•••H-O-H hydrogen bonding. In chapter 5, halogen bonding is discussed in the context of the thyroid system. In particular halogen bonding between a thyroxine iodine atom and the protein backbone as well as crystal water molecules is the subject of this chapter. The effect of substitution of the iodine atom with an astatine atom is presented. Chapter 6 is concerned with halogen bonding in halogenated DNA base pairs. Interaction energies are compared with those of the canonical base pairs, and the effect of halogen bonding on geometry is also discussed. For each system, halogen bonding was found to become stronger and more tolerant of non- linear bond angles going down the halogen group.

The technology employed by human beings for the generation, storage and usage of energy is presently undergoing the fastest and most profound change since the industrial revolution. The changes in the generation and usage of energy necessitate the development of new methods of energy storage. In these systems, electrochemical energy storage will play a crucial role and to this end new electrolytes need to be explored to complement these changes. One such class of liquids is ionic liquids, a class of salts that are molten at room temperature. These liquids have a broad applicability to batteries and supercapacitors. This thesis details work where molecular dynamics simulations have been used to explore the nanostructure of ionic liquids and their mixtures with various molecular solvents at simplistic electrodes. The thesis has two broad sections. The first is covered in Chapter 3, and explores the nanostructure of ionic liquid propylene carbonate solutions, developing a framework through which these nanostructures can be understood. The section concludes that the increasing dilution of ionic liquids decreases the surface charge at which the characteristic ionic liquid oscillatory interfacial structure gives way to a different structure featuring monotonic charge decay. The behaviour of ionic liquids at interfaces is found to be correlated to ion size and type, as well as concentration. A wide divergence in the observed behaviour is shown at positive and negative electrodes due to the asymmetry of propylene carbonate. The second section, consisting of two chapters, explores the interfacial nanostructure of solvate ionic liquids using two different boundary conditions to model the electrode. This work is the first simulation of solvate ionic liquids at electrified interfaces. This section will explore the effect of electrode model on the behaviour of these ionic liquids at the electrode. Chapter 4 uses a fixed charge electrode, whereas Chapter 5 uses one with a fixed potential. The section concludes that regardless of electrode model, the idealised portrait of a solvate ionic liquid - one where the liquid behaves exactly as an aprotic ionic liquid - is not applicable. In Chapter 4's exploration of fixed charged electrodes, the formation of 2 glyme to lithium complexes contradicts the idealised portrait of the liquid. A different change is observed in Chapter 5's exploration of fixed potential electrodes, with both lithium glyme and lithium anion clusters forming at the interface. The key difference between the two studies is that lithium does not coordinate to the electrode in the fixed charge simulations, while in the fixed potential case it does. At the end of Chapter 5 the results are compared against experimental data, with the efficacy of the two models discussed. The aim of both studies is to look at the nanostructure of ionic liquids, when the symmetry between co-ion and cation repulsion - and related effects - is broken by the presence of a non ionic constituent in the liquid.

abstract: The absorption spectra of metal-centered phthalocyanines (MPc's) have been investigated since the early 1960's. With improved experimental techniques to characterize this class of molecules the band assignments have advanced. The characterization remains difficult with historic disagreements. A new push for characterization came with a wave of interest in using these molecules for absorption/donor molecules in organic photovoltaics. The use of zinc phthalocyanine (ZnPc) became of particular interest, in addition to novel research being done for azaporphyrin analogs of ZnPc. A theoretical approach is taken to research the excited states of these molecules using time-dependent density functional theory (TDDFT). Most theoretical results for the first excited state in ZnPc are in only limited agreement with experiment (errors near 0.1 eV or higher). This research investigates ZnPc and 10 additional porphyrin analogs. Excited-state properties are predicted for 8 of these molecules using ab initio computational methods and symmetry breaking for accurate time- dependent self-consistent optimization. Franck-Condon analysis is used to predict the Q-band absorption spectra for all 8 of these molecules. This is the first time that Franck-Condon analysis has been reported in absolute units for any of these molecules. The first excited-state energy for ZnPc is found to be the closest to experiment thus far using a range-separated meta-GGA hybrid functional. The theoretical results are used to find a trend in the novel design of new porphyrin analog molecules. / Dissertation/Thesis / Doctoral Dissertation Materials Science and Engineering 2014

abstract: One of the greatest problems facing society today is the development of a sustainable, carbon neutral energy source to curb the reliance on fossil fuel combustion as the primary source of energy. To overcome this challenge, research efforts have turned to biology for inspiration, as nature is adept at inter-converting low molecular weight precursors into complex molecules. A number of inorganic catalysts have been reported that mimic the active sites of energy-relevant enzymes such as hydrogenases and carbon monoxide dehydrogenase. However, these inorganic models fail to achieve the high activity of the enzymes, which function in aqueous systems, as they lack the critical secondary-shell interactions that enable the active site of enzymes to outperform their organometallic counterparts. To address these challenges, my work utilizes bio-hybrid systems in which artificial proteins are used to modulate the properties of organometallic catalysts. This approach couples the diversity of organometallic function with the robust nature of protein biochemistry, aiming to utilize the protein scaffold to not only enhance rates of reaction, but also to control catalytic cycles and reaction outcomes. To this end, I have used chemical biology techniques to modify natural protein structures and augment the H2 producing ability of a cobalt-catalyst by a factor of five through simple mutagenesis. Concurrently I have designed and characterized a de novo peptide that incorporates various iron sulfur clusters at discrete distances from one another, facilitating electron transfer between the two. Finally, using computational methodologies I have engineered proteins to alter the specificity of a CO2 reduction reaction. The proteins systems developed herein allow for study of protein secondary-shell interactions during catalysis, and enable structure-function relationships to be built. The complete system will be interfaced with a solar fuel cell, accepting electrons from a photosensitized dye and storing energy in chemical bonds, such as H2 or methanol. / Dissertation/Thesis / Doctoral Dissertation Biochemistry 2016

abstract: The exceptional mechanical properties of polymers with heterogeneous structure, such as the high toughness of polyethylene and the excellent blast-protection capability of polyurea, are strongly related to their morphology and nanoscale structure. Different polymer microstructures, such as semicrystalline morphology and segregated nanophases, lead to coordinated molecular motions during deformation in order to preserve compatibility between the different material phases. To study molecular relaxation in polyethylene, a coarse-grained model of polyethylene was calibrated to match the local structural variable distributions sampled from supercooled atomistic melts. The coarse-grained model accurately reproduces structural properties, e.g., the local structure of both the amorphous and crystalline phases, and thermal properties, e.g., glass transition and melt temperatures, and dynamic properties: including the vastly different relaxation time scales of the amorphous and crystalline phases. A hybrid Monte Carlo routine was developed to generate realistic semicrystalline configurations of polyethylene. The generated systems accurately predict the activation energy of the alpha relaxation process within the crystalline phase. Furthermore, the models show that connectivity to long chain segments in the amorphous phase increases the energy barrier for chain slip within crystalline phase. This prediction can guide the development of tougher semicrystalline polymers by providing a fundamental understanding of how nanoscale morphology contributes to chain mobility. In a different study, the macroscopic shock response of polyurea, a phase segregated copolymer, was analyzed using density functional theory (DFT) molecular dynamics (MD) simulations and classical MD simulations. The two models predict the shock response consistently up to shock pressures of 15 GPa, beyond which the DFT-based simulations predict a softer response. From the DFT simulations, an analysis of bond scission was performed as a first step in developing a more fundamental understanding of how shock induced material transformations effect the shock response and pressure dependent strength of polyurea subjected to extreme shocks. / Dissertation/Thesis / Doctoral Dissertation Mechanical Engineering 2017

Made available in DSpace on 2015-05-14T13:21:23Z (GMT). No. of bitstreams: 1 arquivototal.pdf: 2208268 bytes, checksum: a713e84bf72b1325038dab0816e190d4 (MD5) Previous issue date: 2009-11-27 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / In this work the origin of the π−π-staking conformation stability of 5S in the 8-acrylate phenylmenthol 5 was revisiting. The geometries of 5S and 5T conformers were optimized from HF method and the MPW1B95 functional; and the geometries of the 11S and 11T conformers have been optimized from HF, MP2 methods and MPW1B95 functional. All calculations were performed on 6-311 + + G (2d, 2p) 6d as level of calculation. Using the optimized geometries of 5S, 5T, 11S and 11T (from MPW1B95/6-311 + + G (2d, 2p) 6d), were performed 15 energy single-point calculations, investigating various computational methods (ab initio, DFT and semiempirical). We also described the spectroscopic (1H NMR) and theoretical (DFT and ab initio) studies of 3-naphytylpropylcrotonate (12) and 3- naphytylpropylsorbate (21). The geometries of 12S and 12T conformers have been optimized from MP2, HF methods and B3LYP, LSDA and MPW1B95 functionals using 6-311+G(d,p) as calculation level. Finally, we describe the synthesis of 12 and 21 (the unpublished) in 3 steps of each synthesis (19% and 22% respectively of total yields) and the trans geometries of 12T and 21T were characterized as the most stable in the conformational equilibrium of 12 and 21. / Neste trabalho a origem do motivo para a maior estabilidade da conformação de 5S no acrilato de 8-fenilmentol 5 foi investigada. As geometrias dos confôrmeros 5S e 5T foram otimizadas nos métodos HF e no funcional MPW1B95; e as geometrias dos confôrmeros 11S e 11T foram otimizadas nos métodos HF, MP2 e o funcional MPW1B95. Todos os cálculos usaram 6-311++G(2d,2p)6d como nível de cálculo. Usando as geometrias otimizadas de 5S, 5T, 11S e 11T (por MPW1B95/6-311++G(2d,2p)6d), foram efetuados 15 cálculos de energia no ponto, investigando metodologias computacionais variadas (ab initio, DFT e semiempirico). Descrevemos também o estudo espectroscópico (RMN 1H) e teórico (DFT e ab initio) do crotonato de 3-naftilpropila (12) e o sorbato de 3-naftilpropila (21). As geometrias dos confôrmeros de 12S e 12T foram otimizadas com os métodos MP2, HF e os Funcionais B3LYP, LSDA e MPW1B95 usando 6- 311+G(d,p) como nível de cálculo. Finalmente, descrevemos a síntese total de 12 e 21 (inéditas na literatura) em 3 etapas de síntese cada (19% e 22% respectivamente de rendimentos globais) e caracterizamos por 1H RMN a geometria trans 12T e 21T como a mais estável no equilíbrio conformacional de 12 e 21.